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class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> </div> <div id="model-that-can-also-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> <a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></a>Model that can also be solved with Eigenvalues</h2> <p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p> <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/Sys.which.html">Sys.which</a></span>(<span class="st">"gcc"</span>)</a></code></pre></div> <pre><code>## gcc ## "/usr/bin/gcc"</code></pre> <p>First, we build a simple degradation model for a parent compound with one metabolite.</p> <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb3-2" title="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> <a class="sourceLine" id="cb3-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> <a class="sourceLine" id="cb3-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p> <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span>(rbenchmark)) {</a> <a class="sourceLine" id="cb5-2" title="2"> b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span>(</a> <a class="sourceLine" id="cb5-3" title="3"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> <a class="sourceLine" id="cb5-4" title="4"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a> <a class="sourceLine" id="cb5-5" title="5"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> <a class="sourceLine" id="cb5-6" title="6"> <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> <a class="sourceLine" id="cb5-7" title="7"> <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> <a class="sourceLine" id="cb5-8" title="8"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> <a class="sourceLine" id="cb5-9" title="9"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> <a class="sourceLine" id="cb5-10" title="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> <a class="sourceLine" id="cb5-11" title="11"> <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(b<span class="fl">.1</span>)</a> <a class="sourceLine" id="cb5-12" title="12"> factor_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/Round.html">round</a></span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> <a class="sourceLine" id="cb5-13" title="13">} <span class="cf">else</span> {</a> <a class="sourceLine" id="cb5-14" title="14"> factor_SFO_SFO <-<span class="st"> </span><span class="ot">NA</span></a> <a class="sourceLine" id="cb5-15" title="15"> <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)</a> <a class="sourceLine" id="cb5-16" title="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", ## use_compiled = FALSE, : Observations with value of zero were removed from ## the data</code></pre> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = ## TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", ## use_compiled = FALSE, : Observations with value of zero were removed from ## the data ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", ## use_compiled = FALSE, : Observations with value of zero were removed from ## the data ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", ## use_compiled = FALSE, : Observations with value of zero were removed from ## the data</code></pre> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = ## TRUE): Observations with value of zero were removed from the data ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = ## TRUE): Observations with value of zero were removed from the data ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = ## TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self ## 3 deSolve, compiled 3 3.143 1.000 3.142 0 ## 1 deSolve, not compiled 3 29.169 9.281 29.154 0 ## 2 Eigenvalue based 3 4.358 1.387 4.356 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 ## 2 0 0</code></pre> <p>We see that using the compiled model is by a factor of around 9 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> <a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2> <p>This evaluation is also taken from the example section of mkinfit.</p> <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span>(rbenchmark)) {</a> <a class="sourceLine" id="cb14-2" title="2"> FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> <a class="sourceLine" id="cb14-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> <a class="sourceLine" id="cb14-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a> <a class="sourceLine" id="cb14-5" title="5"></a> <a class="sourceLine" id="cb14-6" title="6"> b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span>(</a> <a class="sourceLine" id="cb14-7" title="7"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a> <a class="sourceLine" id="cb14-8" title="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> <a class="sourceLine" id="cb14-9" title="9"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> <a class="sourceLine" id="cb14-10" title="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> <a class="sourceLine" id="cb14-11" title="11"> <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(b<span class="fl">.2</span>)</a> <a class="sourceLine" id="cb14-12" title="12"> factor_FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/Round.html">round</a></span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> <a class="sourceLine" id="cb14-13" title="13">} <span class="cf">else</span> {</a> <a class="sourceLine" id="cb14-14" title="14"> factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span></a> <a class="sourceLine" id="cb14-15" title="15"> <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a> <a class="sourceLine" id="cb14-16" title="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = ## TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = ## TRUE): Observations with value of zero were removed from the data ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = ## TRUE): Observations with value of zero were removed from the data ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = ## TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self ## 2 deSolve, compiled 3 4.840 1.000 4.837 0 ## 1 deSolve, not compiled 3 54.338 11.227 54.309 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> <p>Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.49.6 on</p> <pre><code>## R version 3.6.1 (2019-07-05) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 10 (buster)</code></pre> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#model-that-can-also-be-solved-with-eigenvalues">Model that can also be solved with Eigenvalues</a></li> <li><a href="#model-that-can-not-be-solved-with-eigenvalues">Model that can not be solved with Eigenvalues</a></li> </ul> </div> </div> </div> <footer><div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> </div> </body> </html>